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Nucleic Acids Res. Feb 25, 1993; 21(4): 1007–1011.
PMCID: PMC309236

Intermolecular mRNA-rRNA hybridization and the distribution of potential interaction regions in murine 18S rRNA.


Intermolecular hybridization experiments show that murine 18S rRNA and 28S rRNA are capable of forming stable hybrid structures with mRNA from genes p53, c-myc and c-mos from the same species. Both 5'-uncoding and coding oncogene p53 mRNA regions contain fragments interacting with rRNA. Computer analysis revealed 18S rRNA fragments complementary to oligonucleotides frequently met in mRNA, which are potential hybridization regions (clinger-fragments). The distribution of clinger-fragments along 18S rRNA sequence is universal at least for one hundred murine mRNA sequences analyzed. Maximal frequencies of oligonucleotides complementary to 18S rRNA clinger-fragments are reliably (2-3 times) higher for mRNA than for intron sequences and randomly generated sequences. The results obtained suggest a possible role of clinger-fragments in translation processes as universal regions of mRNA binding.

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Selected References

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  • Shine J, Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. [PMC free article] [PubMed]
  • Jacob WF, Santer M, Dahlberg AE. A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4757–4761. [PMC free article] [PubMed]
  • Hui A, de Boer HA. Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4762–4766. [PMC free article] [PubMed]
  • Min KT, Kim MH, Lee DS. Search for the optimal sequence of the ribosome binding site by random oligonucleotide-directed mutagenesis. Nucleic Acids Res. 1988 Jun 10;16(11):5075–5088. [PMC free article] [PubMed]
  • Weiss RB, Dunn DM, Dahlberg AE, Atkins JF, Gesteland RF. Reading frame switch caused by base-pair formation between the 3' end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli. EMBO J. 1988 May;7(5):1503–1507. [PMC free article] [PubMed]
  • Dahlberg AE. The functional role of ribosomal RNA in protein synthesis. Cell. 1989 May 19;57(4):525–529. [PubMed]
  • Trifonov EN. Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences. J Mol Biol. 1987 Apr 20;194(4):643–652. [PubMed]
  • Göringer HU, Hijazi KA, Murgola EJ, Dahlberg AE. Mutations in 16S rRNA that affect UGA (stop codon)-directed translation termination. Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6603–6607. [PMC free article] [PubMed]
  • Sargan DR, Gregory SP, Butterworth PH. A possible novel interaction between the 3'-end of 18 S ribosomal RNA and the 5'-leader sequence of many eukaryotic messenger RNAs. FEBS Lett. 1982 Oct 18;147(2):133–136. [PubMed]
  • Hagenbüchle O, Santer M, Steitz JA, Mans RJ. Conservation of the primary structure at the 3' end of 18S rRNA from eucaryotic cells. Cell. 1978 Mar;13(3):551–563. [PubMed]
  • Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987 Apr;162(1):156–159. [PubMed]
  • Melton DA, Krieg PA, Rebagliati MR, Maniatis T, Zinn K, Green MR. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 1984 Sep 25;12(18):7035–7056. [PMC free article] [PubMed]
  • Lehrach H, Diamond D, Wozney JM, Boedtker H. RNA molecular weight determinations by gel electrophoresis under denaturing conditions, a critical reexamination. Biochemistry. 1977 Oct 18;16(21):4743–4751. [PubMed]
  • Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. [PMC free article] [PubMed]
  • Maizel JV, Jr, Lenk RP. Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7665–7669. [PMC free article] [PubMed]
  • Raynal F, Michot B, Bachellerie JP. Complete nucleotide sequence of mouse 18 S rRNA gene: comparison with other available homologs. FEBS Lett. 1984 Feb 27;167(2):263–268. [PubMed]
  • Jenkins JR, Rudge K, Redmond S, Wade-Evans A. Cloning and expression analysis of full length mouse cDNA sequences encoding the transformation associated protein p53. Nucleic Acids Res. 1984 Jul 25;12(14):5609–5626. [PMC free article] [PubMed]
  • Stanton LW, Fahrlander PD, Tesser PM, Marcu KB. Nucleotide sequence comparison of normal and translocated murine c-myc genes. Nature. 1984 Aug 2;310(5976):423–425. [PubMed]
  • Van Beveren C, van Straaten F, Galleshaw JA, Verma IM. Nucleotide sequence of the genome of a murine sarcoma virus. Cell. 1981 Nov;27(1 Pt 2):97–108. [PubMed]
  • Van Beveren C, Galleshaw JA, Jonas V, Berns AJ, Doolittle RF, Donoghue DJ, Verma IM. Nucleotide sequence and formation of the transforming gene of a mouse sarcoma virus. Nature. 1981 Jan 22;289(5795):258–262. [PubMed]
  • Chan YL, Gutell R, Noller HF, Wool IG. The nucleotide sequence of a rat 18 S ribosomal ribonucleic acid gene and a proposal for the secondary structure of 18 S ribosomal ribonucleic acid. J Biol Chem. 1984 Jan 10;259(1):224–230. [PubMed]

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